3N1X - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   X-RAY CRYSTAL STRUCTURE OF TOLUENE/O-XYLENE MONOOXYGENASE HYDROXYLASE T201C MUTANT

Authors :   M. H. Sazinsky, M. S. Mccormick, S. J. Lippard

Date :   17 May 10 (Deposition) - 13 Oct 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (2x)
Biol. Unit 2: A,B,C  (1x)

Keywords :   Diiron, 4-Helix Bundle, Carboxylate Bridge, Metalloenzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. J. Song, M. S. Mccormick, R. K. Behan, M. H. Sazinsky, W. Jiang, J. Lin C. Krebs, S. J. Lippard
Active Site Threonine Facilitates Proton Transfer During Dioxygen Activation At The Diiron Center Of Toluene/O-Xylen Monooxygenase Hydroxylase.
J. Am. Chem. Soc. V. 132 13582 2010
PubMed-ID: 20839885 | Reference-DOI: 10.1021/JA1063795

Molecule 1 - TOLUENE O-XYLENE MONOOXYGENASE COMPONENT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET22B(+)
	Gene	:	TOUA
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	320855
	Strain	:	OX1
	Synonym	:	TOLUENE/O-XYLENE MONOOXYGENASE ALPHA SUBUNIT

Molecule 2 - TOLUENE O-XYLENE MONOOXYGENASE COMPONENT
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET22B(+)
	Gene	:	TOUE
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	320855
	Strain	:	OX1
	Synonym	:	TOLUENE/O-XYLENE MONOOXYGENASE BETA SUBUNIT

Molecule 3 - TOLUENE O-XYLENE MONOOXYGENASE COMPONENT
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET22B(+)
	Gene	:	TOUB
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	320855
	Strain	:	OX1
	Synonym	:	TOLUENE/O-XYLENE MONOOXYGENASE GAMMA SUBUNIT

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A	B	C
Biological Unit 2 (1x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	FE	2	Ligand/Ion	FE (III) ION
3	OH	1	Ligand/Ion	HYDROXIDE ION
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	FE	-1	Ligand/Ion	FE (III) ION
3	OH	-1	Ligand/Ion	HYDROXIDE ION
4	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	FE	-1	Ligand/Ion	FE (III) ION
3	OH	-1	Ligand/Ion	HYDROXIDE ION
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:104 , GLU A:134 , HIS A:137 , FE A:500 , OH A:501 , EDO A:502 , HOH A:503	BINDING SITE FOR RESIDUE FE A 499
2	AC2	SOFTWARE	GLU A:134 , GLU A:197 , GLU A:231 , HIS A:234 , FE A:499 , OH A:501 , EDO A:502	BINDING SITE FOR RESIDUE FE A 500
3	AC3	SOFTWARE	GLU A:134 , HIS A:137 , GLU A:231 , HIS A:234 , FE A:499 , FE A:500 , EDO A:502 , HOH A:503	BINDING SITE FOR RESIDUE OH A 501
4	AC4	SOFTWARE	GLU A:104 , GLU A:134 , PHE A:196 , GLU A:197 , FE A:499 , FE A:500 , OH A:501	BINDING SITE FOR RESIDUE EDO A 502
5	AC5	SOFTWARE	LYS B:318 , ARG B:322	BINDING SITE FOR RESIDUE SO4 B 331

(no "SS Bond" information available for 3N1X)

Asymmetric Unit

No.	Residues
1	Gln A:460	-	Pro A:461

(no "SAP(SNP)/Variant" information available for 3N1X)

(no "PROSITE Motif" information available for 3N1X)

(no "Exon" information available for 3N1X)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:491
 aligned with Q6IV66_9PSED | Q6IV66 from UniProtKB/TrEMBL  Length:498

    Alignment length:491
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491 
         Q6IV66_9PSED     2 SMLKREDWYDLTRTTNWTPKYVTENELFPEEMSGARGISMEAWEKYDEPYKITYPEYVSIQREKDSGAYSIKAALERDGFVDRADPGWVSTMQLHFGAIALEEYAASTAEARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANVKRSRKWDWAHKAIHTNEWAAIAARSFFDDMMMTRDSVAVSIMLTFAFETGFTNMQFLGLAADAAEAGDHTFASLISSIQTDESRHAQQGGPSLKILVENGKKDEAQQMVDVAIWRSWKLFSVLTGPIMDYYTPLESRNQSFKEFMLEWIVAQFERQLLDLGLDKPWYWDQFMQDLDETHHGMHLGVWYWRPTVWWDPAAGVSPEEREWLEEKYPGWNDTWGQCWDVITDNLVNGKPELTVPETLPTICNMCNLPIAHTPGNKWNVKDYQLEYEGRLYHFGSEADRWCFQIDPERYENHTNLVDRFLKGEIQPADLAGALMYMSLEPGVMGDDAHDYEWVKAYQ 492
               SCOP domains d3n1xa_ A: Toluene, o-xylene monooxygenase oxygenase subunit TouA                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------Phenol_Hydrox-3n1xA01 A:17-251                                                                                                                                                                                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------YHS-3n1xA02 A:405-448                       -------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh........hhhhhhhhhhhh....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhh..................hhhhh......eee..eee...hhhhhhhhhhhhhhhh...hhhhhhhh......hhhhhhhhh.............hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n1x A   2 SMLKREDWYDLTRTTNWTPKYVTENELFPEEMSGARGISMEAWEKYDEPYKITYPEYVSIQREKDSGAYSIKAALERDGFVDRADPGWVSTMQLHFGAIALEEYAASTAEARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANVKRSRKWDWAHKAIHTNEWAAIAARSFFDDMMMTRDSVAVSIMLTFAFETGFCNMQFLGLAADAAEAGDHTFASLISSIQTDESRHAQQGGPSLKILVENGKKDEAQQMVDVAIWRSWKLFSVLTGPIMDYYTPLESRNQSFKEFMLEWIVAQFERQLLDLGLDKPWYWDQFMQDLDETHHGMHLGVWYWRPTVWWDPAAGVSPEEREWLEEKYPGWNDTWGQCWDVITDNLVNGKPELTVPETLPTICNMCNLPIAHTPGNKWNVKDYQLEYEGRLYHFGSEADRWCFQIDPERYENHTNLVDRFLKGEIQPADLAGALMYMSLEPGVMGDDAHDYEWVKAYQ 492
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491

Chain B from PDB  Type:PROTEIN  Length:324
 aligned with Q6IV62_9PSED | Q6IV62 from UniProtKB/TrEMBL  Length:330

    Alignment length:324
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326    
         Q6IV62_9PSED     7 EALKPLKTWSHLAGNRRRPSEYEVVSTNLHYFTDNPERPWELDSNLPMQTWYKKYCFDSPLKHDDWNAFRDPDQLVYRTYNLLQDGQESYVQGLFDQLNDRGHDQMLTREWVETLARFYTPARYLFHALQMGSVYIHQIAPASTITNCATYETADHLRWLTHTAYRTRELANCYPDVGFGKRERDVWENDPAWQGFRELIEKALIAWDWGEAFTAINLVTKPAVEEALLQQLGSLAQSEGDTLLGLLAQAQKRDAERHRRWSSALVKMALEKEGNREVLQKWVAKWEPLADKAIEAYCSALPDGENAIVEAKSASRYVRQMMGL 330
               SCOP domains d3n1xb_ B: Toluene, o-xylene monooxygenase oxygenase subunit TouE                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------Phenol_Hydrox-3n1xB01 B:56-281                                                                                                                                                                                                    ------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh......hhhhhhhh..................hhhhhhhhhhh........hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n1x B   7 EALKPLKTWSHLAGNRRRPSEYEVVSTNLHYFTDNPERPWELDSNLPMQTWYKKYCFDSPLKHDDWNAFRDPDQLVYRTYNLLQDGQESYVQGLFDQLNDRGHDQMLTREWVETLARFYTPARYLFHALQMGSVYIHQIAPASTITNCATYETADHLRWLTHTAYRTRELANCYPDVGFGKRERDVWENDPAWQGFRELIEKALIAWDWGEAFTAINLVTKPAVEEALLQQLGSLAQSEGDTLLGLLAQAQKRDAERHRRWSSALVKMALEKEGNREVLQKWVAKWEPLADKAIEAYCSALPDGENAIVEAKSASRYVRQMMGL 330
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326

Chain C from PDB  Type:PROTEIN  Length:85
 aligned with Q6IV65_9PSED | Q6IV65 from UniProtKB/TrEMBL  Length:86

    Alignment length:85
                                    11        21        31        41        51        61        71        81     
         Q6IV65_9PSED     2 ATFPIMSNFERDFVIQLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIFMDN  86
               SCOP domains d3n1xc_ C: Toluene, o-xylene monooxygenase oxygenase subunit TouB                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains TmoB-3n1xC01 C:2-85                                                                 - Pfam domains
         Sec.struct. author .eeeeeeee......eeeeee...hhhhhhhhhhh.............eeeeee...........hhhhh......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 3n1x C   2 ATFPIMSNFERDFVIQLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIFMDN  86
                                    11        21        31        41        51        61        71        81

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "CATH Domain" information available for 3N1X)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Phenol_Hydrox (21)

Pseudomonas sp. OX1 (4)

1a	Phenol_Hydrox-3n1xB01	B:56-281
1b	Phenol_Hydrox-3n1xA01	A:17-251

Clan: TRASH (61)

Family: YHS (8)

Pseudomonas sp. OX1 (4)

YHS-3n1xA02

A:405-448

Clan: Ubiquitin (279)

Family: TmoB (8)

Pseudomonas sp. OX1 (4)

TmoB-3n1xC01

C:2-85

Asymmetric Unit(hide GO term definitions)

Chain A (Q6IV66_9PSED | Q6IV66)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0006725	cellular aromatic compound metabolic process	The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Chain B (Q6IV62_9PSED | Q6IV62)

molecular function
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016709	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and one atom of oxygen is incorporated into one donor.
biological process
	GO:0006725	cellular aromatic compound metabolic process	The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Chain C (Q6IV65_9PSED | Q6IV65)

molecular function
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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	Ligands, Modified Residues, Ions
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		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gln A:460 - Pro A:461	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3n1x
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1t0q	WILD-TYPE FORM OF THE SAME PROTEIN AT 2.15 RESOLUTION
2inc	WILD-TYPE FORM OF THE SAME PROTEIN AT 1.85 RESOLUTION
2ind	MN(II) RECONSTITUTED FORM OF THE SAME PROTEIN WITH NO MUTATIONS
2rdb	THE SAME PROTEIN WITH ILE-100 MUTATED TO TRP IN THE HYDROXYLASE ALPHA SUBUNIT
3n1y
3n1z
3n20

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 3)

CATH Domains (0, 0)

Pfam Domains (3, 4)

Gene Ontology (6, 12)

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